An in - silico perspective on the role of methylation-related genes in wheat - Fusarium graminearum interaction

Wheat (Triticum aestivum L.), a vital cereal crop, provides over 20% of the total calories and protein in the human diet. However, Fusarium graminearum, the pathogen responsible for Fusarium head blight (FHB), poses a significant threat to wheat production by contaminating grains with harmful mycotoxins. Although Fusarium head blight is currently a minor disease in India, it has the potential to cause substantial yield and quality losses, especially if rain occurs during mid-anthesis. Epigenetic mechanisms, including DNA methylation and sRNA accumulation, are crucial in regulating gene expression and enabling plants to adapt to environmental stresses. Previous studies investigating wheat's response to F. graminearum through transcriptome analysis of lines differing in 2DL FHB resistance QTLs did not fully explore the role of methylation-related genes. To address this gap, we re-analyzed RNA-Seq data to uncover the response of methylation-related genes to pathogen infection. Our analysis revealed that 16 methylation-related genes were down-regulated in the susceptible line 2-2890, with Gene Ontology (GO) analysis linking these genes to L-methionine salvage from methylthioadenosine (GO:0019509), S-adenosylmethionine metabolism (GO:0033353), and steroid biosynthesis (GO:0006694) (p-value = 0.001). Co-expression analysis identified a negative correlation (-0.82) between methionine S-methyl-transferase (MSM; TraesCS1A02G013800) and 3-hydroxy-3-methyl-glutaryl coenzyme A reductase (HMGCR; TraesCS5A02G269300). HMGCR also showed negative correlations (-1.00) with genes encoding pathogenesis-related, detoxification proteins, and xylanase inhibitors, with GO associating these genes with methionine S-methyl transferase activity (p-value = 0.001). In pathogen-inoculated samples, the elevated expression of HMGCR (Log2 3.25-4.00) and the suppression of MSM (Log2 1.25-3.25) suggest a dual role in stress response and susceptibility, potentially linked to disrupted DNA methylation and isoprenoid biosynthesis pathways. Furthermore, 43 genes down-regulated by miR9678 were associated with biotic stimulus responses and glucan endo-1,4-beta-glucanase activity, highlighting the complex regulatory networks involved in wheat's defense against F. graminearum. This study reveals the roles of methylation-related genes in susceptible wheat lines 2-2890, providing new insights into their potential impact on pathogen response and plant susceptibility.